There is 2312-2291=21 more atoms in your structure file than in the
topology file. If it is due to genion, it shall be less. There might be
other mistakes in previous steps.
Anyway, to make them match, just count how many molecules you have in
the system. The last section in your top file shall be something like
[ molecules ]
Protein X
SOL X
K+ X
Match the number there. Commands like
grep SOL ABC.gro | wc
or
grep Mg ABC.gro | wc
or
grep POT ABC.gro | wc
shall be your good companion.
Regards,
Yang Ye
On 6/10/2007 8:42 AM, Sheyore Omovie wrote:
Thanks,
But this is my first real simulation, So I'll appreciate it if you can
tell me how to determine the number of ions to add with genion.
Thanks
John
From: Alan Dodd <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[email protected]>
To: Discussion list for GROMACS users <[email protected]>
Subject: Re: [gmx-users] Coordinate file does not match topology
Date: Thu, 7 Jun 2007 23:26:01 -0700 (PDT)
Small errors like that are usually down to things like running genion
and not changing the .top. I think I made a problem for myself once
with non-consecutive atom numbering, too.
----- Original Message ----
From: Mark Abraham <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users <[email protected]>
Sent: Friday, June 8, 2007 3:48:28 AM
Subject: Re: [gmx-users] Coordinate file does not match topology
Sheyore Omovie wrote:
> Dear gromacs users,
> While trying to preprocess my files with grompp, i got the ff error
> message:
> "Number of coordinates in coordinate file (b4em.gro, 2312) does not
> match topology (twopolypeptide.top, 2291)"
> How can I fix this?
Make them match. Assuming you haven't managed a gross mismatch of files,
your [molecules] section of your .top probably isn't right. Chapter five
of the manual is your friend here.
Mark
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